Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d32317438c407799c2b33364af6e553fa03fbdfa https://github.com/galaxyproject/galaxy/commit/d32317438c407799c2b33364af6e5... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py
Log Message: ----------- Add build endpoints to user api
Commit: 814d58f9810283c1e851b6c6ec062ab3cb0784bf https://github.com/galaxyproject/galaxy/commit/814d58f9810283c1e851b6c6ec062... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Remove empty lines, reduce comments
Commit: c12c2d1dff45afe1a62321f45a26e2de2d696a99 https://github.com/galaxyproject/galaxy/commit/c12c2d1dff45afe1a62321f45a26e... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Add potential len files to response for now, might move to client-side further down the road
Commit: 72fb0d6f043e5085323059f80a39a9c2fab43b88 https://github.com/galaxyproject/galaxy/commit/72fb0d6f043e5085323059f80a39a... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Fix error handling for build deletion
Commit: 32a8633f4e0b4fc06ba3b61027ae3127cd0c7ece https://github.com/galaxyproject/galaxy/commit/32a8633f4e0b4fc06ba3b61027ae3... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js
Log Message: ----------- Add link to user preference page, return exception if chrom count failed
Commit: 2153ef5b76a1958c0067abb6c5492d1df6767c3c https://github.com/galaxyproject/galaxy/commit/2153ef5b76a1958c0067abb6c5492... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map
Log Message: ----------- Add route for custom builds
Commit: d42848ec9b73a89e1cbe20a3250481bd1b41a93a https://github.com/galaxyproject/galaxy/commit/d42848ec9b73a89e1cbe20a325048... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: A client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Add client view for custom builds, add api endpoint for builds metadata
Commit: 0b26d561aabdb5af6e21e8d845f15325e18d8751 https://github.com/galaxyproject/galaxy/commit/0b26d561aabdb5af6e21e8d845f15... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js
Log Message: ----------- Align style of table view component to other ui views
Commit: 689560d7db23240df193fc913d8165643eea8cac https://github.com/galaxyproject/galaxy/commit/689560d7db23240df193fc913d816... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Implement and connect client add request with endpoint
Commit: 06f61927b5f9f6d35c7c0bdebdd330bae56f6710 https://github.com/galaxyproject/galaxy/commit/06f61927b5f9f6d35c7c0bdebdd33... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Fix delete request, fix error triggered by attempting invalid conversions
Commit: 8b5e27aaeae1ac9b35b0959f2cccaa6988d69163 https://github.com/galaxyproject/galaxy/commit/8b5e27aaeae1ac9b35b0959f2ccca... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Add name validator
Commit: d2692dc77bdd4db48cbcc77d9cd776e0cd7e8bab https://github.com/galaxyproject/galaxy/commit/d2692dc77bdd4db48cbcc77d9cd77... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Sort custom builds in table
Commit: b1b87358e7fdb991cf1ef1b90aabfc8d182304b1 https://github.com/galaxyproject/galaxy/commit/b1b87358e7fdb991cf1ef1b90aabf... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Reset form after submission, highlight missing/failed chrom count
Commit: 200b3837c7956e4ee5b19b01eb67e62375e58e97 https://github.com/galaxyproject/galaxy/commit/200b3837c7956e4ee5b19b01eb67e... Author: guerler aysam.guerler@gmail.com Date: 2017-03-15 (Wed, 15 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js
Log Message: ----------- Remove debug statements for user preferences
Commit: 15273ad1489c9cdc216126ff36c2ec2d912e4165 https://github.com/galaxyproject/galaxy/commit/15273ad1489c9cdc216126ff36c2e... Author: guerler aysam.guerler@gmail.com Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Add uploader element
Commit: bb5b8cf525562e1a930ad03a4071dffd341865e5 https://github.com/galaxyproject/galaxy/commit/bb5b8cf525562e1a930ad03a4071d... Author: guerler aysam.guerler@gmail.com Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js
Log Message: ----------- Declare submit caller for upload element
Commit: 474b0c1d2ceade095fd995d19ba30334be612458 https://github.com/galaxyproject/galaxy/commit/474b0c1d2ceade095fd995d19ba30... Author: guerler aysam.guerler@gmail.com Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Sort models in table, fix message parameter, properly return models with count attribute
Commit: 39c9f79970579556eac63c12d40174ee95e2c337 https://github.com/galaxyproject/galaxy/commit/39c9f79970579556eac63c12d4017... Author: guerler aysam.guerler@gmail.com Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Improve error handling, add success and warning messages
Commit: 4180d2e08841628753a65966143c58d6c5630d90 https://github.com/galaxyproject/galaxy/commit/4180d2e08841628753a65966143c5... Author: guerler aysam.guerler@gmail.com Date: 2017-03-16 (Thu, 16 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Fix success message
Commit: f5844252ae9feee554342e69562c3ae65985bb82 https://github.com/galaxyproject/galaxy/commit/f5844252ae9feee554342e69562c3... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Attempt to determine line count upon file upload to allow early validation
Commit: aea96855bb5da18623c51ab6e6885f5c9acaf19e https://github.com/galaxyproject/galaxy/commit/aea96855bb5da18623c51ab6e6885... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Merge branch 'add_uploader' into remove_custom_builds_mako
Commit: e78e1607db1eacc175c8f731cdb879fe3e293476 https://github.com/galaxyproject/galaxy/commit/e78e1607db1eacc175c8f731cdb87... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js
Log Message: ----------- Upload and preview file using HTML5, client-side file reader
Commit: b557e31a4c29fcab875837c1ccc3c9cd9f37f6ba https://github.com/galaxyproject/galaxy/commit/b557e31a4c29fcab875837c1ccc3c... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Fix form reset, remove debug statements
Commit: abe156783a7305a8341e217ece31500c36631232 https://github.com/galaxyproject/galaxy/commit/abe156783a7305a8341e217ece315... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Set default to fasta selection
Commit: 95b6f033a447d25b5826a4e368caf2fc15201d10 https://github.com/galaxyproject/galaxy/commit/95b6f033a447d25b5826a4e368caf... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Display installed builds as searchable list
Commit: 6b2a4ebd3653f25ef01e109ac7bdad601d6959a5 https://github.com/galaxyproject/galaxy/commit/6b2a4ebd3653f25ef01e109ac7bda... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Len-file hdas not needed in metadata
Commit: 39c1b1b24998d9ce77d660ad5dee525f71156720 https://github.com/galaxyproject/galaxy/commit/39c1b1b24998d9ce77d660ad5dee5... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Render len type help section
Commit: 76bcf23b434984cd45002192a72bb90d3c06ade5 https://github.com/galaxyproject/galaxy/commit/76bcf23b434984cd45002192a72bb... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Add help section content
Commit: ad73c7d39d93683aba1b065b6660c4b5a98554bf https://github.com/galaxyproject/galaxy/commit/ad73c7d39d93683aba1b065b6660c... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: R templates/user/dbkeys.mako
Log Message: ----------- Remove mako
Commit: 5ee585c681326072c489f26d2d2b084a6995a349 https://github.com/galaxyproject/galaxy/commit/5ee585c681326072c489f26d2d2b0... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Remove controller endpoint
Commit: ff5166c2930f54a05601ab9a934319689df9c3f8 https://github.com/galaxyproject/galaxy/commit/ff5166c2930f54a05601ab9a93431... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js
Log Message: ----------- Redirect masthead link to new custom builds ui
Commit: a89a4f726ba60110810c99b372a53b48e9152c4e https://github.com/galaxyproject/galaxy/commit/a89a4f726ba60110810c99b372a53... Author: guerler aysam.guerler@gmail.com Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Revise style
Commit: 72c96bd5c6c6c3c1dea3a662dd2fa2d802822401 https://github.com/galaxyproject/galaxy/commit/72c96bd5c6c6c3c1dea3a662dd2fa... Author: guerler aysam.guerler@gmail.com Date: 2017-03-18 (Sat, 18 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js
Log Message: ----------- Hide select field if local fields are unavailable
Commit: 7873aac2edb003fa073efc1249884d7b25c9028f https://github.com/galaxyproject/galaxy/commit/7873aac2edb003fa073efc1249884... Author: guerler aysam.guerler@gmail.com Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M .ci/py3_sources.txt M README.rst A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png R doc/source/admin/grt.rst R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst R doc/source/admin/webhooks.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst M doc/source/project/issues.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml R lib/galaxy/util/postfork.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run_tests.sh M scripts/api/README M scripts/secret_decoder_ring.py A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M test/api/test_libraries.py M test/docker/base/run_test_wrapper.sh
Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako
Commit: 2872a31881f2f404b2962464ffb734065e96d1b3 https://github.com/galaxyproject/galaxy/commit/2872a31881f2f404b2962464ffb73... Author: guerler aysam.guerler@gmail.com Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/style/less/ui.less M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js M static/style/blue/base.css
Log Message: ----------- Move styles out of code file
Commit: 2fc18675dbfd66a296006bb4ef90d57bdde4d5dc https://github.com/galaxyproject/galaxy/commit/2fc18675dbfd66a296006bb4ef90d... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Debug
Commit: 71b09b49a7541789909b1617e661e0252573453a https://github.com/galaxyproject/galaxy/commit/71b09b49a7541789909b1617e661e... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Fix label, fix dataset id parsing
Commit: ef2353a1423586845da9d19c5780f298db742b1c https://github.com/galaxyproject/galaxy/commit/ef2353a1423586845da9d19c5780f... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Add len id for converted datasets to dbkey attributes
Commit: afbb3b5a1e26a0a3e9698cec71ed5d733189d451 https://github.com/galaxyproject/galaxy/commit/afbb3b5a1e26a0a3e9698cec71ed5... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Add additional error message for fasta conversions
Commit: 368b276ded599e7f0c206b852cdd901199b16b7e https://github.com/galaxyproject/galaxy/commit/368b276ded599e7f0c206b852cdd9... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Parse correct dataset id
Commit: 50283125ea37f313afdfd0d69b92a0380fc77e17 https://github.com/galaxyproject/galaxy/commit/50283125ea37f313afdfd0d69b92a... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py
Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako
Commit: 76bd515879d4353bff066d0b2526d68d86cdff56 https://github.com/galaxyproject/galaxy/commit/76bd515879d4353bff066d0b2526d... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message: ----------- Fix lint
Commit: b0325cef02f995a589dc14425d1ae73d7ef4cfee https://github.com/galaxyproject/galaxy/commit/b0325cef02f995a589dc14425d1ae... Author: guerler aysam.guerler@gmail.com Date: 2017-03-22 (Wed, 22 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Post determine fasta results
Commit: 3b7d44e6f7b773218fad0820464efa4610130938 https://github.com/galaxyproject/galaxy/commit/3b7d44e6f7b773218fad0820464ef... Author: guerler aysam.guerler@gmail.com Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css
Log Message: ----------- Fix message margin in left column
Commit: 4a0f00fc1e3f383450968a9732edb479378f82ac https://github.com/galaxyproject/galaxy/commit/4a0f00fc1e3f383450968a9732edb... Author: guerler aysam.guerler@gmail.com Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Trigger jobs when custom build has been added, check for linecount file on reload
Commit: 95be12787ace869bf01f6c30e4b62ba7a4739c96 https://github.com/galaxyproject/galaxy/commit/95be12787ace869bf01f6c30e4b62... Author: guerler aysam.guerler@gmail.com Date: 2017-03-23 (Thu, 23 Mar 2017)
Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M lib/galaxy/jobs/runners/__init__.py M run_tests.sh M static/maps/layout/menu.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M test/qunit/package.json
Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako
Commit: 81824fa0446a6f4f5c372961528609d362e5fbfa https://github.com/galaxyproject/galaxy/commit/81824fa0446a6f4f5c37296152860... Author: guerler aysam.guerler@gmail.com Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_tools.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py
Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako
Commit: 452683998293d525e4c999d6ebf6f5eb85adca2e https://github.com/galaxyproject/galaxy/commit/452683998293d525e4c999d6ebf6f... Author: guerler aysam.guerler@gmail.com Date: 2017-03-29 (Wed, 29 Mar 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/users.py
Log Message: ----------- Annotate new api endpoints
Commit: 31a8ebe9d5e6595ea0299546b59c07ce32931ac0 https://github.com/galaxyproject/galaxy/commit/31a8ebe9d5e6595ea0299546b59c0... Author: guerler aysam.guerler@gmail.com Date: 2017-03-30 (Thu, 30 Mar 2017)
Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py
Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako
Commit: 405dbd3b7f3022332fb6c660f88e67361fbb5429 https://github.com/galaxyproject/galaxy/commit/405dbd3b7f3022332fb6c660f88e6... Author: guerler aysam.guerler@gmail.com Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js
Log Message: ----------- Move custom build metadata endpoint to histories
Commit: a16c5320fd647b45dbad197714fc52d2a5254548 https://github.com/galaxyproject/galaxy/commit/a16c5320fd647b45dbad197714fc5... Author: guerler aysam.guerler@gmail.com Date: 2017-04-04 (Tue, 04 Apr 2017)
Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/api/histories.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map
Log Message: ----------- Wait for history panel, workaround until overall ui has been visited
Commit: d607c7e0b134ac81faf0648af6e8a48d8941c938 https://github.com/galaxyproject/galaxy/commit/d607c7e0b134ac81faf0648af6e8a... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-04-05 (Wed, 05 Apr 2017)
Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako
Log Message: ----------- Merge remote-tracking branch 'guerler/remove_custom_builds_mako' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/8bbd423909d7...d607c7e0b134